To the best of my knowledge, the issue is never directly addressed. The rules, on a quick scan, appear the same as in 3.5, where this issue has been debated some as well.
The long and short of the argument is this: the statement in shadow evocation et al. is that someone who knows that it is fake does not need to save. Nothing says he does not save or may not save, just that he doesn’t have to. This is taken to mean that this is optional, and effectively someone in this position has the option of automatically succeeding on his save the same way you typically have the option of failing any save. You may, according to this logic, choose not to automatically succeed, and then, since you are now attempting a saving throw, choose to automatically fail.
Strict-RAW, this seems most accurate, though it definitely takes a few steps to get there and it’s clearly not written out explicitly. Still, the language, whether it was intended to be or not, is precise: it waives a requirement to save, it does not add a requirement to not-save.
Whether or not you should rule this way in your game is more dubious. Shadow evocation et al. are rather useful, particularly for this feature. In 3.5, greater shadow evocation was typically used to cover the loss of contingency due to the banning of Evocation as a specialist wizard. In Pathfinder, this is less of an issue (since banning is no longer so absolute anyway). Most of the time, shadow evocation et al. are most useful when the drawbacks of using them (the Will save, the quasi-reality) don’t actually affect the functioning of the spell, which is precisely in this case: buffing. Ultimately, it becomes yet another powerful and flexible tool in the wizard’s toolbox, and he’s already got a ton of those. Shadow evocation et al. are’t the most powerful of them, but maybe it’s worthwhile to you to start paring down options where you can.
While spell attacks are affected by the unseen attackers rule (PHB 194) as any other attack, saving throws follow different rules. In the general rules for saving throws we read that:
A saving throw can be modified by a situational bonus or penalty and
can be affected by advantage and disadvantage, as determined by the DM. (PHB 179)
But while it is left up to the DM, there is also the arcane trickster feature magical ambush:
if you are hidden from a creature when you cast a spell on it, the
creature has disadvantage on any saving throw it makes against the
spell this turn. (PHB 98)
It is strongly implied that this is a special rule overwriting the general case. Granting this to all characters (and NPC-s) would make this feature redundant.
There are not many features that grant disadvantage on saving throws. The above rogue feature is acquired on level 9, and the sorcerer metamagic that does it is generally the most the expensive one. It is clear that such a thing should be regarded as really powerful. Consider that traps also grant a saving throw as normal, even though they need no components to cast and are usually hidden.
Thus I advise against ruling that being hidden should grant disadvantage on saving throws.
Best Answer
A "special resistance to magic" referred to abilities other than spell resistance
In the D&D 3.5e Player's Handbook the description of this mechanic helpfully includes an example of a special resistance to magic:
This text didn't survive into the SRD (such examples were widely removed to incentivise acquiring the actual PHB), so it didn't make it directly into Pathfinder, and Paizo didn't add any other examples in its stead. However, it seems that in the original source, it was meant to be the case that a spell's target could voluntarily be affected by things they would normally be immune to - such as an elf suppressing their immunity to magical sleep in order to be affected by a spell - and it does not generally refer to spell resistance, which has separate rules for voluntarily suppressing.
Neither 3.5e nor Pathfinder's rules and published books seem to mention this particular mechanic ever again, so there's no other examples or explanation to draw upon that could clarify further.
In any event, spell resistance and saving throws are separate things; if a spell does not overcome a creature's spell resistance, they aren't subject to a saving throw in the first place, so they can't voluntarily fail it. A creature would have to both actively lower their spell resistance and passively deliberately fail the resulting saving throw in order to guarantee being affected by such a spell.